AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i002_Purine_Nucleotides_Metabolism_mgen_reg_100.orf -o002_mgen_100.ace -a/home/amcguire/alignace/lib/ORF_mgen.txt -z/skink1/amcguire/genomes/mgen.fna -g0.32 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG00101	91	Mycoplasma

Motif number 1

 CGTGCGCATAACGATGCTTGATAACATTG	1	10	1	AACGATGCTT	     0.98253	-82
GATGCTTGATAACATTGCTTTGAACATGAT	1	23	1	AACATTGCTT	    0.997733	-69
CATTGCTTTGAACATGATTTTTAATTATTT	1	35	1	AACATGATTT	    0.988771	-57
GTTTTATTAAAACATTATTTAATAATAAAT	1	61	0	AACATTATTT	    0.994754	-31
     ATTGCAATATTGTTTTATTAAAACA	1	77	0	AATATTGTTT	    0.988159	-15
          **********

Masking position 2
Map Score:   10.6416

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 96
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TGCTTTGAACATGATTTTTAATTATTTATT	1	38	1	ATGATTTTTA	    0.960108	-54
ATGATTTTTAATTATTTATTATTAAATAAT	1	48	1	ATTATTTATT	    0.954967	-44
TTATTAAAACATTATTTAATAATAAATAAT	1	58	0	ATTATTTAAT	    0.734689	-34
  ATTGCAATATTGTTTTATTAAAACATTA	1	74	0	ATTGTTTTAT	    0.980304	-18
          **********

Masking position 5
Map Score:   4.69653

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 69
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

          **********

No masking
Map Score:   9.48026e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

          **********

No masking
Map Score:   9.48026e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   9.48026e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0